701 research outputs found
String Matching with Multicore CPUs: Performing Better with the Aho-Corasick Algorithm
Multiple string matching is known as locating all the occurrences of a given
number of patterns in an arbitrary string. It is used in bio-computing
applications where the algorithms are commonly used for retrieval of
information such as sequence analysis and gene/protein identification.
Extremely large amount of data in the form of strings has to be processed in
such bio-computing applications. Therefore, improving the performance of
multiple string matching algorithms is always desirable. Multicore
architectures are capable of providing better performance by parallelizing the
multiple string matching algorithms. The Aho-Corasick algorithm is the one that
is commonly used in exact multiple string matching algorithms. The focus of
this paper is the acceleration of Aho-Corasick algorithm through a multicore
CPU based software implementation. Through our implementation and evaluation of
results, we prove that our method performs better compared to the state of the
art
The IUPUI Signature Center on Bio-Computing
poster abstractBio-Computing is the discipline that integrates biomedical concepts and Computer Science techniques for collecting, managing, processing and analyzing large-scale biomedical data, as well as enables a deeper understanding of biological processes and medical procedures through modeling, simulation, and visualization. Bio-Computing emphasizes the algorithmic, computational, and software system issues arising from biomedical problems. It focuses on developing new, improved, specialized and customized Computer Science techniques and tools for computing related needs in life science applications that do not have ready-to-use solutions. The IUPUI Signature Center on Bio-Computing (SCBC) aims to act as a catalyst to provide BioComputing infrastructure and expertise for Indiana life science initiative. The specific mission is the following:
β’ Bio-Computing Infrastructure: To develop cutting-edge bio-computing techniques and tools to establish an infrastructure as a framework to support life science applications.
β’ Collaborative Projects: To actively engage in collaborative research projects, and maximize the impact of bio-computing in life science research and funding efforts. The scope of the projects supported by SCBC can be best described by the figure below
New Method of Measuring TCP Performance of IP Network using Bio-computing
The measurement of performance of Internet Protocol IP network can be done by
Transmission Control Protocol TCP because it guarantees send data from one end
of the connection actually gets to the other end and in the same order it was
send, otherwise an error is reported. There are several methods to measure the
performance of TCP among these methods genetic algorithms, neural network, data
mining etc, all these methods have weakness and can't reach to correct measure
of TCP performance. This paper proposed a new method of measuring TCP
performance for real time IP network using Biocomputing, especially molecular
calculation because it provides wisdom results and it can exploit all
facilities of phylogentic analysis. Applying the new method at real time on
Biological Kurdish Messenger BIOKM model designed to measure the TCP
performance in two types of protocols File Transfer Protocol FTP and Internet
Relay Chat Daemon IRCD. This application gives very close result of TCP
performance comparing with TCP performance which obtains from Little's law
using same model (BIOKM), i.e. the different percentage of utilization (Busy or
traffic industry) and the idle time which are obtained from a new method base
on Bio-computing comparing with Little's law was (nearly) 0.13%.
KEYWORDS Bio-computing, TCP performance, Phylogenetic tree, Hybridized Model
(Normalized), FTP, IRCDComment: 17 Pages,10 Figures,5 Table
Application of Neural-Like P Systems With State Values for Power Coordination of Photovoltaic/Battery Microgrids
The power coordination control of a photovoltaic/battery microgrid is performed with a novel
bio-computing model within the framework of membrane computing. First, a neural-like P system with
state values (SVNPS) is proposed for describing complex logical relationships between different modes
of Photovoltaic (PV) units and energy storage units. After comparing the objects in the neurons with the
thresholds, state values will be obtained to determine the con guration of the SVNPS. Considering the
characteristics of PV/battery microgrids, an operation control strategy based on bus voltages of the point of
common coupling and charging/discharging statuses of batteries is proposed. At rst, the SVNPS is used to
construct the complicated unit working modes; each unit of the microgrid can adjust the operation modes
automatically. After that, the output power of each unit is reasonably coordinated to ensure the operation
stability of the microgrid. Finally, a PV/battery microgrid, including two PV units, one storage unit, and
some loads are taken into consideration, and experimental results show the feasibility and effectiveness of
the proposed control strategy and the SVNPS-based power coordination control models
Evolutionary algorithms: Overview and applications to European transport
The present paper aims to analyse the research potential of Evolutionary Algorithms (EAs) in the light of their possible applications in the space-economy. For this purpose the first part of the paper will be devoted to an overview and illustration of EAs, also in comparison with other recent tools emerging form bio-computing, like Neural Networks (NNs). The second part of the paper will then focus on empirical applications concerning analyses and forecasts of European freight transport flows (at a regional level). In this context, the results stemming from an integrated approach combining EAs with NNs will be compared with those from conventional methodologies, like logit models, as well as with the "usual" NN models. We will analyze the sensitivity of various results by using different environmental policy on scenarios on European transport. The empirical experiments highlight the advantages and limitations of these approaches from both a methodological and empirical viewpoint, by offering a plausible range of values of outcomes that may be useful for planners and operators in this field.
Nanoengineered polymeric capsules for bio-computing
Β© 2015 AIP Publishing LLC. Nanoengineered polymeric capsules are currently widely used in the drug design sector. In this paper, we present data, allowing to consider this objects as important elements of bio-computers, allowing, in particular, targeted delivery and smart release of the "main program" (special molecular preparations) to zones, where the adequate functioning of the system can be affected by undesirable events
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Όλ¬Έ (λ°μ¬)-- μμΈλνκ΅ λνμ : μμ°κ³Όνλν ννλΆ, 2019. 2. λ¨μ’λ―Ό.Supported lipid bilayer is a two-dimensional lipid bilayer self-assembled on a hydrophilic substrate with two-dimensional fluidity. By introducing plasmonic nanoparticles with strong scattering signals into the supported lipid bilayer, it is possible to observe and track thousands of nanoparticles and their interactions at a single-nanoparticle level in real time. In this thesis, I expand the nanoparticle-lipid bilayer platform by engineering plasmonic nanoparticles to construct a complex nanoparticle network system and develop multiplexed bio-detection and bio-computing strategies.
Chapter 1 describes a supported lipid bilayer platform incorporating plasmonic nanoparticles. Section 1 introduces the optical properties and biosensing application of plasmonic nanoparticles, and Section 2 introduces tethering technique, characteristics, and advantages for introducing nanoparticles into supported lipid bilayer platforms. In Chapter 2, I introduce a system that can distinguish nine types of nanoparticle assembly reactions occurring simultaneously by introducing optically encoded plasmonic nanoparticles that scatter red, blue, and green light into supported lipid bilayers. I performed multiplexed detection of nine types of microRNAs, which are important gene regulators and cancer cell biomarker. In Chapter 3, I develop a bio-computing platform that recognizes molecular inputs, performs logic circuits, and generates nanoparticle assembly/disassembly output signals. Complex logic circuits are designed and implemented by combining two strategies: (i) interfacial design that constructs a logic circuit through DNA functionalization of the interface of nanoparticles, and (ii) a network design that connects assembly/disassembly reactions. In Chapter 4, I develop a bio-computing calculator capable of performing arithmetic logic operations. I use the nanoparticle-lipid bilayer platform as the hardware that stores, processes, and outputs information, and constructs software that contains logic circuit functions through DNA solution. An information storage nanoparticle stores solution-phase molecular input signals on the surface of nanoparticles. The bio-computing lipid nanotablet recognizes an arithmetic logic circuit programmed with DNA information and generates outputs a result of a kinetic difference between nanoparticle assembly reaction according to the storage state of the input signal.μ§μ§ν μ§μ§ μ΄μ€μΈ΅μ μΉμμ± κΈ°ν μμ 쑰립λ 2μ°¨μμ μ§μ§ μ΄μ€μΈ΅μΌλ‘ 2μ°¨μ μμ μ λμ±μ κ°μ§λ€. μ§μ§ν μ§μ§ μ΄μ€μΈ΅μ κ°ν μ°λ μ νΈλ₯Ό μ§λλ νλΌμ¦λͺ¨λ λλ
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μ κ²°ν© λ°μμ λ°μμλμ μ°¨μ΄λ₯Ό μΌμΌν€κ³ κ²°κ³Όλ₯Ό μΆλ ₯νλ€.Chapter 1. Introduction: Plasmonic Nanoparticle-Tethered Supported Lipid Bilayer Platform 1
1.1. Plasmonic Nanoparticles and Their Bio-Applications 2
1.1.1. Introduction 4
1.1.2. Fundamentals of Plasmonic Nanoparticles 8
1.1.3. Plasmonic Nanoparticle Engineering for Biological Application 11
1.1.4. Plasmonic Nanoparticles for Rayleigh Scattering-Based Biosensing 16
1.1.5. References 21
1. 2. Supported Lipid Bilayer as a Dynamic Platform 24
1.2.1. Introduction 26
1.2.2. Basic Setups and Strategies 29
1.2.3. Nanoparticle-Tethering Techniques 33
1.2.4. Real-Time Imaging and Tracking of Single Nanoparticles on SLB 39
1.2.5. Observation of Interactions between Single Nanoparticles 44
1.2.6. References 50
Chapter 2. Multiplexed Biomolecular Detection Strategy 53
2.1. Introduction 55
2.2. Experimental Section 60
2.3. Results and Discussion 66
2.4. Conclusion 77
2.5. Supporting Information 79
2.6. References 83
Chapter 3. Nano-Bio Computing on Lipid Bilayer 84
3.1. Introduction 85
3.2. Experimental Section 88
3.3. Results and Discussion 98
3.4. Conclusion 120
3.5. Supporting Information 124
3.6. References 161
Chapter 4. Development of Nanoparticle Architecture for Biomolecular Arithmetic Logic Operation 163
4.1. Introduction 165
4.2. Experimental Section 167
4.3. Results and Discussion 171
4.4. Conclusion 177
4.5. References 179
Abstract in Korean 180Docto
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